Contacts of the strand formed by residues 205 - 214 (chain E) in PDB entry 3CB4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 205 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E PHE* 3.7 16.2 - - - -
201E ASP* 2.9 41.7 + - - +
203E TYR 3.4 2.2 + - - -
204E LEU* 1.3 78.8 - - - +
206E VAL* 1.3 65.5 + - - -
207E VAL* 3.3 0.9 + - - +
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Residues in contact with VAL 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E SER* 4.7 2.5 - - - -
199E TRP 3.6 10.5 - - - +
200E PHE* 3.8 15.2 - - + -
204E LEU 4.2 0.4 + - - +
205E GLY* 1.3 71.2 - - - -
207E VAL* 1.3 69.2 + - - +
208E SER* 4.6 8.1 - - - +
258E LEU 4.2 5.7 - - - +
259E VAL* 4.3 7.8 - - - +
260E CYS 4.1 13.2 + - - +
262E ILE* 3.2 41.0 + - + +
263E LYS 3.8 1.3 - - - +
264E ASP* 3.6 30.1 - - - +
265E ILE* 3.9 22.9 - - + +
268E ALA* 5.0 2.7 - - + -
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Residues in contact with VAL 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E SER* 3.4 2.6 - - - -
199E TRP* 2.9 66.8 + - + +
201E ASP* 3.7 18.2 - - + +
204E LEU* 4.0 12.6 - - + -
205E GLY 3.4 14.8 - - - +
206E VAL* 1.3 75.5 - - - +
208E SER* 1.3 63.7 + - - +
244E GLN* 5.3 4.0 - - - +
257E TRP* 4.0 20.6 - - + -
258E LEU 3.6 10.3 - - - +
259E VAL* 3.8 18.8 - - + -
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Residues in contact with SER 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ILE* 4.6 11.9 - - - -
197E ASP 3.4 4.7 - - - -
198E SER* 3.0 19.3 + - - -
199E TRP* 4.4 4.0 - - - -
206E VAL* 4.6 3.3 - - - +
207E VAL* 1.3 75.3 - - - +
209E LEU* 1.3 61.7 - - - +
210E ILE* 4.0 8.0 + - - -
257E TRP* 3.2 7.3 - - - +
258E LEU* 2.9 39.8 + - - -
262E ILE* 4.8 4.7 - - - +
268E ALA* 3.3 19.1 - - - +
274E LEU* 5.5 3.3 - - - +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E GLN* 3.7 20.9 - - + +
58E SER* 3.4 35.4 - - - +
76E ILE* 5.0 3.8 - - + -
194E LEU 3.6 0.3 - - - +
195E ILE* 3.7 3.8 - - - +
196E ILE* 2.8 57.2 + - + -
197E ASP* 2.7 20.4 + - + +
199E TRP* 3.8 12.3 - - + -
208E SER* 1.3 71.7 - - - +
210E ILE* 1.3 57.5 + - - +
240E PHE* 4.1 17.3 - - + -
255E VAL* 4.1 8.7 - - + -
256E GLY* 3.4 23.3 - - - +
257E TRP* 4.6 0.2 - - - -
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Residues in contact with ILE 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E ALA* 3.4 27.8 - - + -
194E LEU 3.3 7.0 - - - +
195E ILE* 5.3 1.1 - - + -
196E ILE* 3.7 4.5 - - - -
208E SER* 4.5 6.5 - - - +
209E LEU* 1.3 77.7 - - - +
211E ARG* 1.3 68.7 + - - +
212E ILE* 3.7 11.9 - - + -
217E LEU* 4.2 14.1 - - + -
250E LEU* 4.9 6.5 - - + -
255E VAL* 3.2 10.7 - - - +
256E GLY 2.7 39.0 + - - +
258E LEU* 3.4 45.1 - - + +
274E LEU* 3.7 17.0 - - + -
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Residues in contact with ARG 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 5.4 0.2 - - - +
6E ASN* 3.3 12.1 - - - +
94E ALA* 3.2 46.6 + - + +
96E GLU* 2.6 42.0 + - - -
183E PRO* 3.4 12.0 - - - +
184E GLU 4.6 5.1 + - - +
193E ALA* 3.3 2.4 - - - -
194E LEU* 2.8 41.8 + - + +
196E ILE* 3.7 5.1 - - + +
210E ILE* 1.3 77.1 - - - +
212E ILE* 1.3 83.7 + - - +
213E LYS* 3.3 34.5 + - + +
253E GLY* 3.7 10.0 - - - -
254E GLU 3.5 4.5 - - - -
255E VAL* 3.8 16.4 - - + -
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Residues in contact with ILE 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E LEU* 4.4 4.3 - - + -
192E GLN 4.1 2.0 - - - -
193E ALA* 4.1 7.6 - - + +
210E ILE* 3.7 19.7 - - + -
211E ARG* 1.3 79.3 + - - +
213E LYS* 1.3 57.8 + - - +
214E ASN 3.6 12.8 - - - +
215E GLY 3.4 27.4 - - - +
216E THR* 4.7 0.2 - - - -
217E LEU* 4.1 16.2 - - + -
250E LEU* 3.6 32.3 - - + +
251E LYS 3.5 20.6 - - - +
252E CYS* 3.7 9.0 - - - +
253E GLY* 2.8 26.1 + - - +
254E GLU 3.0 13.8 + - - +
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Residues in contact with LYS 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ALA* 2.9 32.5 + - - +
94E ALA* 4.7 3.6 - - - +
95E CYS 5.5 0.8 + - - -
96E GLU* 5.3 2.6 + - - -
184E GLU 3.3 23.0 - - - +
185E GLY* 3.9 0.5 - - - -
192E GLN* 2.9 13.4 + - + +
194E LEU* 4.6 11.9 - - + -
211E ARG* 3.3 31.1 + - - +
212E ILE* 1.3 73.7 - - - +
214E ASN* 1.3 65.7 + - - +
252E CYS* 3.8 5.5 - - - -
285E LEU* 4.0 36.3 - - + -
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Residues in contact with ASN 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E GLY* 3.4 7.1 - - - -
186E ASP* 2.8 31.8 + - - +
189E GLY* 3.9 15.6 - - - -
190E PRO* 3.2 27.9 + - - +
191E LEU* 3.4 8.1 - - - +
192E GLN* 2.9 46.8 + - + +
212E ILE* 3.6 3.8 - - - +
213E LYS* 1.3 77.0 - - - +
215E GLY* 1.3 68.1 + - - +
252E CYS* 4.0 3.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il